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MetaServer
The GeneSilico MetaServer is a gateway to a number of third-party methods for protein structure prediction (identification of domains,
secondary structure prediction, fold-recognition, and finally, 3D model generation). Users can submit a protein sequence (or alignment)
by a single click, then analyze the summary of results generated by many methods, and finally predict the protein structure according
to the "consensus" approach.
FRankenstein3D
This tool builds protein models by recombining fragments of Fold-Recognition alignments. Users can
select a set of alignments from the output of the MetaServer or provide their own alignments. The program will generate alternative
models, identify fragments that either exhibit consensus conformation in different models or - in the absence of consensus - show the
relatively best compatibility of amino acids with the environment of the rest of the model. These fragments will be recombined to
create a hybrid model, which will be further optimized by trying alternative alignments in non-consensus regions to improve the
sequence-structure compatibility.
COLORADO3D
This simple server facilitates visual presentation of three-dimensional (3D) protein structures. It is a gateway to a number of methods
for evaluation of protein structure (ANOLEA, PROSAII, PROVE or VERIFY3D), but also identifies buried residues and depicts sequence
conservation. As an input, it takes a PDB file and, optionally, a multiple sequence alignment. As an output, the server returns a file
in which the B-factor column is replaced with values of the chosen parameter (structure quality, residue burial or conservation). These
values can be visualized as colors using structure viewers such as RASMOL or SWISS PDB VIEWER.
FILTREST3D
This is an "alpha" version of a server for discrimination of a large number of alternative models of protein structure against a set of
restraints derived from low-resolution experimental analyses (such as cross-linking, mutagenesis, circular dichrosm etc.) as well as
from computational predictions (e.g. solvent accessibility, amino acid contact maps).
STRUCLA
While most phylogenetic methods calculate trees based on sequence alignments, this server (STRUcture
CLAssification) allows to use protein structures. The prefereed input is an alignment of protein coordinates exported from SWISS PDB
VIEWER. The user specifies the distance cutoff and selects which measures should be used to calculate the "evolutionary distances"
between the protein structures. The server returns series of unrooted trees in the NEXUS format and corresponding distance matrices, as
well as a consensus tree. This method is most useful in the 'twilight zone of homology', where amino acid sequences are too diverged to
provide reliable relationships.
CompaRNA
The CompaRNA web server provides a continuous benchmark of automated standalone and web server methods for RNA secondary structure
prediction. It has been inspired by the EVA and Livebench servers for benchmarking of protein structure prediction tools, which have
greatly contributed to progress in the field of structural bioinformatics. The aim of CompaRNA is to assess the state of the art in RNA
structure prediction, provide a detailed picture of what is possible with the available tools, where progress is being made and what
major problems remain. The CompaRNA server is a valuable resource for all researchers who focus their attention on the usage and
development of RNA structure prediction methods.
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